We will integrate genome and transcriptome assemblies using new methods and technologies as a novel approach to the decades-old search for cause of X-linked dystonia-parkinsonism (XDP), with implications for unsolved rare disorders and diseases that are specific to isolate populations. XDP is a neurodegenerative disease that combines clinical features of dystonia and Parkinson?s disease (PD), with a neuropathology that resembles Huntington?s disease (HD). XDP is indigenous to the Philippines, and specifically to the island of Panay. Linkage was established to a genomic segment in 1991, yet the causal mutation is unknown. Our Preliminary Studies suggest that prior assumptions about the genetic architecture of this disorder have been limited by conventional technologies. Here, we propose that powerful new genomics tools can solve this long- standing problem through reference-free reconstruction of the XDP haplotype to identify known and cryptic sequences, then to characterize the functional genomic alterations associated with the putative causal variants and the molecular consequences of manipulating those variants in induced pluripotent stem cell (iPSC) derived neural tissues. We will investigate XDP as an exemplar of unsolved Mendelian disorders or those from isolate populations that have likely arisen from a founder haplotype. We propose to determine the exact sequence of the shared haplotype in a small number of multigenerational XDP families by de novo assembly, then to define the complete allelic architecture of the XDP region in a large collection of 500 XDP cases and 1000 controls from Panay, as well as tens of thousands of individuals with neurodegenerative conditions more broadly (Aim 1). We will then compare molecular signatures associated with the XDP haplotype in peripheral and iPSC- derived neural tissue from a well characterized group of 30 XDP cases and matched, unaffected male family members. To attribute the putative causal mutation to these transcriptional signatures, we will perform in vitro modeling with CRISPR/Cas9 to correct the defect in XDP proband lines and introduce it into unaffected male sibling lines, while performing the same analyses for all specific mutations in an isogenic Filipino and Caucasian control lines. We will then evaluate consequent changes to the associated genes and co- expression networks following this perturbation (Aim 2). Finally, we will perform global analyses of genes, pathways, and networks associated with XDP and compare these molecular signatures to other monogenic forms of neurodegenerative disorders from comparable RNAseq datasets, including inherited dystonias, LRRK2-associated PD, and HD, to explore shared and novel molecular mechanisms in these disorders. At its conclusion, this study will reconstruct the XDP haplotype and identify all plausible causal mutations, characterize their molecular consequences, and derive new insights into more common forms of neurodegenerative disorders. It may also establish a roadmap for human disease research in isolate populations that obviates reliance on a single consensus human reference among diverse populations.